Genomics
Genomics is the study of an organism's entire genome. Investigation of single genes, their functions and roles is something very common in today's medical and biological research, and can not be said to be genomics but rather the most typical feature of molecular biology. Genomics can be said to have appeared in the 1980s, and took off in the 1990s with the initiation of genome projects for several species. A major branch of genomics is still concerned with sequencing the genomes of various organisms, although the knowledge of full genomes have created the possibility for the field of functional genomics, mainly concerned with patterns of gene expression during various conditions. The most important tools here are microarrays and bioinformatics. Study of the full set of proteins in a cell type or tissue, and the changes during various condition, is called proteomics. Sequencing genomes In 1972, Walter Fiers and his team at the Laboratory of Molecular Biology of the University of Ghent (Ghent, Belgium) were the first to determine the sequence of a gene: the gene for bacteriophage MS2 coat proteinMin Jou W, Haegeman G, Ysebaert M, Fiers W., Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein, Nature. 1972 May 12;237(5350):82-8. In 1976, Walter Fiers and his team determine the complete nucleotide-sequence of bacteriophage MS2-RNAFiers W et al., Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene, Nature, 260, 500-507, 1976. The first DNA-based genome to be sequenced in its entirety was that of bacteriophage Φ-X174; (5,368 bp), sequenced by Frederick Sanger in 1977Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M., Nucleotide sequence of bacteriophage phi X174 DNA, Nature. 1977 Feb 24;265(5596):687-95. The first free-living organism to be sequenced was that of Haemophilus influenzae (1.8Mb) in 1995, and since then genomes are being sequenced at a rapid pace. A rough draft of the human genome was completed by the Human Genome Project in early 2001 amid much fanfare. As of January 2005, the complete sequence was known of about 1,000 viruses, 220 different bacterial species and roughly 20 eukaryote organisms, of which about half are fungi. Nationalencyklopedin, encyclopaedia in Swedish, the article Genom. Web edition, available only to subscribers Most of the bacteria whose genomes have been sequenced in total are problematic disease-causing agents, such as Haemophilus influenzae. Of the other sequenced species, most were picked because they were well-studied model organisms or because they promised to become good models. Yeast (Saccharomyces cerevisiae) has long been an important model organism for the eukaryotic cell, while the fruit fly Drosophila melanogaster has been a very important tool (notably in early pre-molecular genetics). The worm Caenorhabditis elegans is an often used simple model for multicellular organisms. The zebrafish Brachydanio rerio is used for many developmental studies on the molecular level and the flower Arabidopsis thaliana is a model organism for flowering plants. The Japanese pufferfish (Takifugu rubripes) and the spotted green pufferfish (Tetraodon nigroviridis) are interesting because of their small and compact genomes, containing very little non-coding DNA compared to most species. [http://news.bbc.co.uk/1/hi/sci/tech/3760766.stm BBC article Human gene number slashed from Wednesday, 20 October, 2004] CBSE News, Thursday October 16, 2003 The mammals dog (Canis familiaris) NHGRI, pressrelease of the publishing of the dog genome brown rat (Rattus norvegicus), mouse (Mus musculus), and chimpanzee (Pan troglodytes) are all important model animals in medical research. Comparative genomics Comparison of genomes has resulted in some surprising biological discoveries. If a particular DNA sequence or pattern is present among many members of a clade, that sequence is said to have been conserved among the species. Evolutionary conservation of a DNA sequence may imply that it confers a relative selective advantage to the organisms that possess it. Conservation also suggests that sequence has functional significance. It may be a protein coding sequence or regulatory region. Experimental investigation of some of these sequences has shown that some are transcribed into small RNA molecules, although the functions of these RNAs were not immediately apparent. The identification of similar sequences (including many genes) in two distantly related organisms, but not in other members of one of the clades, has led to the theory that these sequences were acquired by horizontal gene transfer. This phenomenon is most prominent in bacteria, although it also seems that genes were transferred from Archaea to Eubacteria. It has also been noticed that bacterial genes exist in eukaryotic nuclear genomes and that these genes generally encode mitochondrial and plastid proteins, giving support to the endosymbiotic theory of the origin of these organelles. This theory holds that the mitochondria and chloroplast organelles found in many animal and plant genomes were originally free-living bacteria that were absorbed by an ancestral eukaryote, and that subsequently became an integral part of the eukaryotic cell. Euaryota with sequenced genome (2006) : Anopheles gambiae Apis mellifera Arabidopsis thaliana Ashbya gossypii Caenorhabditis briggsae Caenorhabditis elegans Candida glabrata Canis familiaris Ciona intestinalis Cryptosporidium hominis Cryptosporidium parvum Cyanidioschyzon merolae Debaryomyces hansenii Drosophila melanogaster Encephalitozoon cuniculi Gallus gallus Guillardia theta Homo sapiens Kluyveromyces lactis Kluyveromyces waltii Magnaporthe grisea Mus musculus Neurospora crassa Oryza sativa Pan troglodytes Phanerochaete chrysosporium Plasmodium falciparum Plasmodium yoelii yoelii Populus trichocarpa Rattus norvegicus Saccharomyces cerevisiae Schizosaccharomyces pombe Takifugu rubripes Tetraodon nigroviridis Thalassiosira pseudonana Yarrowia lipolytica ENCODE Project HapMap See also * bioinformatics * chemogenomics * DNA motif * gene therapy * genetic engineering * list of omics topics in biology * -omics * pharmaceutical company * proteomics * structural genomics * sequence profiling tool * transcriptomics References Sources and external links * World Health Organization Genomics Resource Centre * Nationalencyklopedin, encyclopaedia in Swedish, articles Genomik and Genom * PLoS Primer: Comparative Genomics * The Paleobiotics Lab * "The Human Genome Issue" Nature, February 15, 2001, no. 6822 * Search Human Gene Information Database - http://www.medicalcomputing.net/cgi-bin/query_human_gene_info, Medical Computing .Net * Genomics Online Database - http://wit.integratedgenomics.com/GOLD * Joint Genome Institute * The Institute for Genomic Research - http://www.tigr.org * The Sanger Institute - http://www.sanger.ac.uk * The National Center for Biotechnology Information - http://www.ncbi.nlm.nih.gov * http://www.dbbm.fiocruz.br/genomics/genomics.html * http://www.dbbm.fiocruz.br/genome/tcruzi/tcruzi.html (Chagas' Disease and Trypanosoma cruzi genome project) * Translational Genomics Research Institute * Australian Centre for Plant Functional Genomics * International Genomics Consortium * Global Musa Genomics Consortium * Functional Annotation of the Mouse database * International Journal of Medical Sciences * Dengueinfo.org - Dengue Virus full genome database - http://www.dengueinfo.org/ * The National Office of Public Health Genomics * NHGRI - http://www.genome.gov/ Category:Genomics ca:Genòmica es:Genómica id:Genomika it:Genomica lt:Genomika ja:ゲノミクス pl:Genomika sv:Genomik zh:基因體學 Bold text